Material Instances with Animation Nodes
At present the method is not to create instances of the material, but to vary vertex color per object. 
Assuming cycles render, cycles allows per object info on the same material as: random, obj index or vertex color.

(For Blender Internal render, there are other methods, it allows object color etc)

Imitating your case, a basic setup looks like this:


instance the object
make sure you have "deep copy" so that each object has a different mesh, (like shiftD manual copy in blender)
color/set vertex color to set vcolor for each object
in cycles use attribute to get that color per object


(note that you don't need to create the vcol before, the node creates it or takes the first existing one)


There are other methods for this simple example. But generally it's better to vary this data than:


having to manage 100 materials only to change a color.
using object index, that may be used in other places, render layers etc
switch 2 materials only for ks for this limited case of pure switch


Also, vcol allows more variations of the color, using combine color node (hsv) to vary hue or any other complex rule.

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Here's an example that uses object index (pass_index) as 0/1 to switch things. 
But this parameter can very well be used in other places and only works with integers (0, 1, 2...100, 200...).

It is not the best. Still, you may need to use this if the object is not a mesh, but a curve or text.
(On texts there are other specific methods too, but for this simplistic switch it's ok)